Peptoid Helices

Fig. 1.7 Illustration of the distinct CD exhibited by peptoid helices containing solely aromatic or solely aliphatic residues. Sample concentrations were 60 p,M in acetonitrile. Spectra were acquired at room temperature.

CD Studies of Longer Peptoid Helices Containing a-Chiral Aromatic Side Chains... 

Wu, C., Sanborn, T., Huang, K., Zuckermann, R., and Barron, A. Peptoid oligomers with alpha-chiral, aromatic side chains Sequence requirements for the formation of stable peptoid helices. /. 

Peptoid helices are detected in structure-supporting solvents even in relatively short oligomers. Because intramolecular C=0- H-N H-bond formation cannot be the driving force for peptoid secondary structure, the steric influence of the bulky and chiral side chain is likely to provide the required constraint. Interactions between side-chain groups, and between side chains and the carbonyls of the main-chain amides, may add stability to the ordered secondary structure. However, for very short oligomers (34) or peptoids based on N-substituted a-amino acids with a small side chain (35), such as Nala (also termed sarcosine, Sar, 9), complex mixtures of conformers associated with either cis or trans tertiary amide groups have been detected. In addition to the classic CD technique, the contribution of other spectroscopies, such as pulsed ESR (36), may be of value for the 3-D structural validation of peptoid molecules. 

Fig. 13 Stabilized helices and nonnatural helix mimetics several strategies that stabilize the a-helical conformation in peptides or mimic this domain with nonnatural scaffolds have been described. Recent advances include [1-peptide helices, terphenyl helix-mimetics, mini-proteins, peptoid helices, side-chain crosslinked a-helices, and the hydrogen bond surrogate (HBS) derived a-helices. Circles represent amino acid side-chain functionality (Reprinted from Henchey et al. [52], Copyright (2008) with permission from Elsevier)...

Peptoids have also been utilized in higher order stmctures. The peptoid helix served as a constmction piece in longer 30-, 45-, and 60-mer peptoid helical btmdles constmcted using native chemical ligation. These helical bundles represent the first examples of peptoid tertiary stmcture and may move peptoids from mimicry of short peptides to longer (though still relatively tiny and simple) proteins, enabling a further expansion in the capabilities of peptoids. 

Zuckermann et al. described a different approach and introduced 1-phenylethyl peptoid side chains with functional groups in the para-position of the phenyl ring (Fig. 7). Thus, the functionalities are present at the outer perimeter of the peptoid helices. As such, it allows mimicking of the interaction between a-helices in coiled coUs and helix bundles in proteins [74-76]. 

Brase, Muhle-Goll and coworkers reported on functional peptoid helices [77]. In order to create cell-penetrating peptoids, butylamine residues were incorporated into peptoids. NMR spectroscopy and molecular modeling revealed an extended pseudo-helical structure with predominant c/s-conformation in the backbone. The electrostatic repulsion between the side chains leads to maximization of the spacing of the ammonium residues and thus dominates the conformation of the peptoid. With a pitch of 7.7 A, the charge distribution is somewhat less dense compared to a-helical peptides. Nevertheless, the peptoids were effective transporters, similar to other cell-penetrating peptides. 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

As such, the magainins provide a useful initial target for peptoid-based peptido-mimetic efforts. Since the helical structure and sequence patterning of these peptides seem primarily responsible for their antibacterial activity and specificity, it is conceivable that an appropriately designed, non-peptide helix should be capable of these same activities. As previously described (Section 1.6.2), peptoids have been shown to form remarkably stable hehces, with physical characterishcs similar to those of peptide polyprohne type-I hehces (e.g. cis-amide bonds, three residues per helical turn, and 6A pitch). A faciaUy amphipathic peptoid helix design, based on the magainin structural motif, would therefore incorporate cationic residues, hydrophobic aromatic residues, and hydrophobic aliphathic residues with threefold sequence periodicity. 

Figure 6 Molecular representation of the left-handed peptoid helix with the cp, oo backbone torsion angles typical of type-1 poly(L-Pro)n.

Figure 15 Variants of peptoid 1 investigated for functional effects of sequence variation. The three-sided peptoid helix is pictorially represented for comparison of different sequences. The C-terminus is on the bottom and the N-terminus is on top. All vertices not otherwise labeled represent Nspe residue, and red charges represent M,ys residues. Blue circles, purple triangles, and green squares represent substitution with proline, and Afedp,...

Kang et al. used a peptoid helix to position porphyrins in different relative orientations. It was found that whether the porphyrins were positioned cofacial, slipped-cofacial, or unstructured had profound effects on the degree of J-aggregation, the resulting color, and excitonic coupling [78]. The authors suggest... 

The more complicated design of tertiary and quaternary stmcture in proteins has been attained in some cases. However, the ability to form hierarchically ordered stmctures, or self-assemble folded stmctural units into well-defined higher order assemblies, from any non-natural backbone remains an important unsolved problem. A few preliminary reports, including work on p-peptides and peptoids, with stmcture beyond the helix were reported recently [20-22]. These two backbones represent the more weU studied sequences of foldamers and so initial reports toward stmctures beyond secondary elements can be expected. However, given more than a decade of foldamer research, little work toward these higher order stmctures has been reported. 

Figure 52 Models of substrate-catalyst interaction, (a) Energy-minimized structure of substrate 1-phenylethanol docked in the cleft of peptoid 141 as viewed perpendicular to the helix axis (Left) and down the helix axis with the N-terminus projecting forward (Right), (b) The substrate 1-phenylethanol approaching the catalytic TEMPO site of the sterically encumbered scaffold of peptoid 143. The ovals represent the reaction site comprising the snbslrate hydroxyl group and TEMPO nitroxyl radical. Color key hy ogen, white oxygen, red nitrogen, blue 1-phenylethanol (substrate), green. (Reprinted with permission from Ref. 190. National Academy of Sciences of the United States, 2009.)...

Bundles of helices are an important feature of tertiary structure in transmembrane proteins and elsewhere. Zuckermann and co-workers used a combinatorial approach to screen 3,400 different 15-mer peptoids for their ability to form aggregates of helices [101]. As a design concept, every third residue unit was chosen from a pool of 12 hydrophobic residues and the remaining monomer units were hydrophilic. Such amphiphilic helices result in structures in which one sector (approximately one third to one half of the outer surface) of the helix is hydrophobic and the rest is hydrophilic (Fig. 11). Hits were identified by fluorescence assay because peptoids that assemble into a structure with a hydrophobic core should... 

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